3OKR

Structure of Mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3okrb_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D	d3okrd_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d3okra_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d3okrc_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8083037	3000077	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8083037	3000077	SCOP2B (2022-06-29)
A	SCOP2 Family	Cytidylytransferase	8083036	4002789	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide-diphospho-sugar transferases	8083037	3000077	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8083037	3000077	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF01128	e3okrB1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: PF01128	ECOD (1.6)
D	PF01128	e3okrD1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: PF01128	ECOD (1.6)
A	PF01128	e3okrA1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: PF01128	ECOD (1.6)
C	PF01128	e3okrC1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: PF01128	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
D	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
A	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
C	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01128	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD)	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding pyrimidine ribonucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleotide binding nucleoside phosphate binding organic cyclic compound binding anion binding pyrimidine ribonucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding CTP binding pyrimidine nucleotide binding manganese ion binding transition metal ion binding zinc ion binding cytidylyltransferase activity 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process lipid biosynthetic process isopentenyl diphosphate biosynthetic process carbohydrate derivative metabolic process terpenoid biosynthetic process glyceraldehyde-3-phosphate metabolic process phospholipid metabolic process organic substance metabolic process cellular aldehyde metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway cellular biosynthetic process lipid biosynthetic process isopentenyl diphosphate biosynthetic process carbohydrate derivative metabolic process terpenoid biosynthetic process glyceraldehyde-3-phosphate metabolic process phospholipid metabolic process organic substance metabolic process cellular aldehyde metabolic process organic substance biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway cellular metabolic process terpenoid biosynthetic process, mevalonate-independent primary metabolic process phospholipid biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process cellular lipid metabolic process metabolic process cellular process isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process terpenoid metabolic process lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process	cell periphery plasma membrane membrane cellular anatomical entity
E [auth F]	Heptamer peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR034683	Cytidylyltransferase IspD/TarI	Family
A, B, C, D	IPR018294	4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site	Conserved Site
A, B, C, D	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, B, C, D	IPR001228	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.